Comparing the applicability of CGE-on-the-chip and SDS-PAGE for fast pre-screening of mouse serum samples prior to proteomics analysis

Abstract

In this comparative study, a set of 13 mouse sera was investigated, which had to be checked in a fast way for homogeneity prior to complex, time-consuming and expensive proteomics analysis. SDS-PAGE and CGE-on-the-chip were compared in terms of handling, time consumption and significance of detecting differences. SDS-PAGE was a system giving good information on the samples at first sight and discrepancies for one sample were observed immediately after staining. The time consumption of up to 20 h was rather high (separation and staining procedure with 14 cm gels) in SDS-PAGE. CGE-on-the-chip system exhibited differences for two samples and, most important, analysis time was reduced to only 1 h. Of importance is that the serum protein pattern obtained by both methods may not represent the same proteins. Sample preparation was equal for both analytical techniques but necessary sample amount was only half of the material in the case of CGE-on-the-chip. Statistical evaluation indicated highly critical values for only one sample in SDS-PAGE and for two samples in the CGE-on-the-chip system, both in good agreement with visual observations. Three samples showed limited homogeneity with both methods. Five and six samples, respectively, were indicated as noticeable with one of the used methods. © 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.